Merge branch 'main' of github.com:MPI-Dortmund/pymissense

README.md

@@ -1,24 +1,22 @@
 [![DOI](https://zenodo.org/badge/697276360.svg)](https://zenodo.org/badge/latestdoi/697276360)
 
 # pymissense
-PyMissense creates the pathogencity plot and modified pdb as shown in the [AlphaMissense paper](https://www.science.org/doi/10.1126/science.adg7492) for custom proteins.
+PyMissense generates the pathogenicity plot and modified pdb as shown in the [AlphaMissense paper](https://www.science.org/doi/10.1126/science.adg7492) for custom proteins.
 
 ## What it does
 
-AlphaMissense allows you to identify regions in your amino acid chain that are critical for protein function. This skript does two things:
+AlphaMissense allows you to identify regions in your amino acid chain that are critical for protein function. This script does two things:
 
 1. It generates a plot similar to [Figure 3D](https://www.science.org/doi/10.1126/science.adg7492#F3) of the [AlphaMissense paper](https://www.science.org/doi/10.1126/science.adg7492)
 
    <img src="resources/img/3d.png" width="400">
 
 
 
-2. It creates a modified PDB file where the temperature factor is replaced by the pathogencity predicted by AlphaMissense that allows you to visualize the effect with Chimerax, like [Figure 3E](https://www.science.org/doi/10.1126/science.adg7492#F3) of the paper:
+2. It generates a modified PDB file where the temperature factor (bfactor) is replaced by the pathogenicity predicted by AlphaMissense, allowing the effect to be visualised with Chimerax, as in [Figure 3E](https://www.science.org/doi/10.1126/science.adg7492#F3) of the paper:
 
    <img src="resources/img/3e.jpeg" width="400">
 
-It does so by replacing the bfactor in the PDB.
-
 ## How to install
 
 ```
@@ -27,7 +25,7 @@ pip install pymissense
 
 ## How to use it
 
-Generate usage is:
+General usage is:
 ```
 usage: pymissense[-h] [--tsv TSV] [--pdbpath PDBPATH] [--maxacid MAXACID] uniprot_id output_path
 
@@ -44,17 +42,17 @@ options:
   --maxacid MAXACID  Maximum squence number to use in the plot. (default: None)
 ```
 
-You can provide the optional argument `--pdbpath` if you want to use an experimental PDB, otherwise it will instead download the alphafold predicted PDB.
+You can give the optional argument `--pdbpath` if you want to use an experimental PDB, otherwise it will download the alphafold predicted PDB instead. With `--tsv` you can provide the decompressed AlphaMissense database, so that pymissense does not need to download it.
 
-For example, to reproduce [Figure 3D](https://www.science.org/doi/10.1126/science.adg7492#F3) (the middle one) and generates the PDB shown in [Figure 3E](https://www.science.org/doi/10.1126/science.adg7492#F3) do:
+For example, to reproduce [Figure 3D](https://www.science.org/doi/10.1126/science.adg7492#F3) (the middle one) and generate the PDB shown in [Figure 3E](https://www.science.org/doi/10.1126/science.adg7492#F3) do:
 
 ```
 wget https://files.rcsb.org/download/7UPI.pdb
 pymissense Q9UQ13 out --maxacid 200 --pdbpath 7upi.pdb 
 ```
 
-Note that they displayed only the first 200 amino acids in the plots and showed the pathogencity with the experimental PDB `7upi`.
+Note that only the first 200 amino acids are shown in the plots and the pathogenicity is shown with the experimental PDB `7upi`.
 
 ## Contributions
 
-This script was developed in collaboration with Tobias Raisch 
+This script was developed in collaboration with Tobias Raisch